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dc.contributor.authorMona Mahmoud Abdien_US
dc.description.abstractDomestic cat breeds exhibit remarkable phenotypic diversity and unique population histories that revolved around the selection of desirable aesthetic traits. In this thesis, two different approaches, population differentiation index (Fst) and integrated haplotype homozygosity score (iHS), were applied to study the landscape of selection within the genomes of cat breeds. The analytical approaches were performed using a comprehensive dataset of 41 cat populations/breeds that were genotyped for ~58K genome-wide autosomal SNP markers. Population structure and breed ancestries were explored using PCA and Admixture analysis. Both PCA and Admixture initially showed three major clusters of cat breeds; (1) Western breeds, (2) Eastern breeds and (3) In-between breeds that were closer to Western breeds. Across breeds, 273 candidate selective sweeps were identified using the Fst-based approach whereas 317 candidate sweeps were localized using the haplotype-based approach. Runs of homozygosity (ROH) were determined within each breed where only 25 breeds exhibited segments of ROH >500kb. Comparative analysis of signals of selection in light of the population structure of cat breeds suggested that signatures of selection were more intense and confined to a smaller region when the breed under investigation is compared to closely related breeds or large number of breeds, which might be due to the minimization the effect of population structure. Annotating the regions harboring candidate selective sweeps revealed a panel of previously identified genes associated with phenotypic traits in cat breeds such as LPAR6, KRT71, KIT, FGF5 and TYR. In addition, other genes (n=5090) were found to reside within the regions under selection and most of which were strongly enriched for nervous system development and regulation. Four genomic regions were highlighted as unique signatures for single breed or multiple related breeds. The four regions were found in ChrB2, ChrB3, ChrB4 and ChrD2 each of which contains 120, 5, 80 and 1 genes, respectively. Overall, 590 genomic regions were identified to be putatively under positive selection in the cat genome across all breeds. Further investigation of genes within the identified regions and the associated biological functions need to be addressed in future studies.en_US
dc.publisher Kuwait university - college of graduate studiesen_US
dc.subjectGenomic : Cat Breedsen_US
dc.titleGenomic Landscape of Selection in Domestic Cat Breedsen_US
dc.contributor.supervisorDr. Hasan Alhaddaden_US
dc.description.conclusionsThis study explored the genomic landscape of selection by means of number of regions, size of regions and their distribution on the genome of 34 domestic cat breeds. Further analysis of gene lists identified by this study may highlight candidate genes that are associated with phenotypic traits under selection in each breed independently or across multiple cat breeds. Many regions left uninvestigated due to the limitation of SNP data used and such regions may harbor important information regarding variation involved in determination of phenotypic traits. Thus, a denser SNP chip or whole sequencing data may allow the detection of additional regions that were not found in this analysis.en_US
Appears in Programs:2050 Molecular Biology
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